If you want to skip every 3rd circle, you can use the modulo operator (%), it gives you the remainder of a division of two values:
for(i = 0 ; i < 12 ; i++){
if (i % 3 == 0) { //3 divided by 3 has remainder 0, also 6, 9, etc.
continue;
} else {
ofSetColor(200);
ofCircle(blackLocX[i], blackLocY[i], pieceR);
}
}